Similar regions between promoters of yocD

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GATGCCATTCATATAGGGGATATAAAAGGCCCTCCGAATCACGGGTTTGGCTCCATTTGC hal ...............GGAGAAAGAAAAGGCAC............GTCTGGCTCCATGAGC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATGAAATATTTAAAAGATATTGCAAGAGACCATAATATACCGAAAGTCACCGGAGACATC hal .......................................................ATATC -240 -230 -220 -210 -200 -190 >>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GCCAAACGG-GATTGGAATCATGTAGACCGGCTGATTCACTTTTATGAAAAACATCACTT hal GGAAAAAGAAGCTCGGCTAAATGTAGATATGGCGATTTAATGGAGGGATAAA........ -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CAAAGTATGTATCGATCATGATACCCAATCCGGCAGCATTAAGTGGGTTGATTTGTAAAA hal ............................................GGAATGATTTTTATTA -120 -110 -100 -90 -80 -70 sub AAGTCTGGAAGAAAGAGCCAAGATATGCTGTAATGGTATAAAACCATTGATGGAGGGTTC hal TGGCATGGCTGAAAGAG..AAAGTAAGCTGACTTGGTGTAAA....TTAATGGAGGGAT. -60 -50 -40 -30 -20 -10 sub T hal . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...